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| Status |
Public on Sep 27, 2022 |
| Title |
HIBD-SB input1 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: brain
treatment: HIBD-SB
strain: Wistar
chip antibody: none (input)
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| Growth protocol |
Wistar rats, 8–10 weeks old, SPF grade, housed in a 12-h light/dark cycle, with free access to food and water.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefy, after deeply anesthetized with chloral hydrate(200 mg/kg), the rats pups in Sham, HIBD and HIBD+SB groups were perfused with physiological saline from the right auricle until the liver turns white. The brain of rats was removed on ice, put into an ice-cold PBS and rapidly separated the infarct side cerebral cortex
Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer’s manual. The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina Novaseq sequencer according to the manufacturer’s recommended protocol.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
rat brain tissue,H3K9cr,PTM
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| Data processing |
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina NovaSeq 6000 sequencer. Firstly, Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality clean reads were generated. Then these clean reads were aligned to rat reference genome (UCSC rn5) using bowtie2 software (v2.2.4) with default parameters. Peak calling was performed with MACS software (v2.2.7.1).
Differentially enriched regions were identified by diffReps software (v1.55.4).
The enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation. GO and KEGG Pathway analysis were performed on the peak-associated genes or differentially enriched peak-associated genes. And the enriched peaks were visualized in UCSC Genome Browser.
Assembly: RN5
Supplementary files format and content: chr: chromosome number of enrichment peak; Start: initial genomic coordinates of enrichment peak; End: terminating genome coordinates of enrichment peak; Peak ID: indicates the MACS peak ID.MACS uses sample VS Input for ChIP enrichment peak recognition, and the default peak with P <= 1E-5 is statistically significant enrichment peak.
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| Submission date |
May 31, 2022 |
| Last update date |
Sep 27, 2022 |
| Contact name |
shan wang |
| E-mail(s) |
wsaquarius@sina.com
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| Organization name |
Capital Institute of Pediatrics
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| Street address |
2yabao road
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| City |
beijing |
| ZIP/Postal code |
100020 |
| Country |
China |
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| Platform ID |
GPL25947 |
| Series (2) |
| GSE205142 |
Sodium Butyrate(SB) mediates Histone Crotonylation and Alleviated Neonatal Rats Hypoxic -Ischemic Brain Injury Through Gut-Brain Axis [ChIP-seq] |
| GSE205144 |
Sodium Butyrate(SB) mediates Histone Crotonylation and Alleviated Neonatal Rats Hypoxic -Ischemic Brain Injury Through Gut-Brain Axis |
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| Relations |
| BioSample |
SAMN28775457 |
| SRA |
SRX15504470 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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